The problem of putting what is galciv into language is because it is more of a feeling being portrayed vs. a set rule-book of what is and what isn't galciv.
To get an idea of this feeling of what is galciv, look at GalCiv 2 and 1. Take what is at the core of those games... GalCiv 1 had you wonder to each star and colonize particular systems and travel the entire map (think endless space without space lanes) for interaction with stars. Then we upped the game to Gal Civ 2, where most people have a well defined image of Galactic Civilizations.
A lot of Galactic Civilizations follows a general 4x rule book. Keep the players time more on the main map vs. any sub-window. The exception to this feature is the shipyard where designing ships can be crucial (but this is not necessary, and can be quick for more users).
The other feature that defines Galactic Civilizations is the fact the map is an abstract of time vs. distance. The number of hexes on the map does not indicate a distance it indicates a time. The space folding works strangely throughout the galaxy and the folding of space moves at varying distances through space. That is also why you have a limited galaxy that you cannot pass a certain point. The way the hyper drive works prevents infinite travel into deep space.
The adjacency bonus fit into Galactic Civilizations as it is a seemless addition to the planet screen. We already had a planet screen where we may place buildlings down, and so in Gal Civ 2, it was a matter of room for the building vs. placement, but there were bonuses that kept the player thinking I want this particular building there. Now, take that to another level if there is a building that provides the same bonuses to adjacent tiles, then it is like there was a resource to take advantage of in that spot. Hence, it was the same idea that was already in Gal Civ 2, but moved to an advanced form. Doing a sim city version of the game moves the game away from 4x standard rulebook of keep these subscreens short. Recall you may have 100+ planets and playing sim city for a short while on 100+ planets would take a long time.
Adding resources to the main map to harvest. That is a new feature and follows more the Civilization idea. It is not a far fetched idea as we were able to mine asteroids and so this is just a simple modification of let us mine for a special resource instead of adding production. The foundation was there it was just improved.
The dual que system of Galactic Civilization. The initial removal of this led to a large uproar here on the forums. Many ideas were thrown out to re instate the dual que. Eventually the idea of the starport was realized to be placed on the map. It fit into lore and provides interesting gameplay role to this game. I would call this a NEW feature entirely and not an improvement on old features so much. The idea of moving the ship building to another much more vunerable structure opens up a lot more strategies and may provide a easy mop-up stage at the end of the game. We'll see when the AI and more play testing are done.
Why is 3D not Gal Civ? For one all known galaxies live on a plane. Although that plane is skewed one direction or the other, they are on the plane. The nature of the Gal Civ is to have a fixed distance points abstracted in large squares / hexes (now) This system would be done in a large 3 Dimensional lattice. One it is Difficult to select an individual cube from a large 3D lattice. Secondly, each system you encounter would be on the plane and so we would have 3 different types of solar systems indicating the directions we have cubes stack in the lattice. Hence, from each solar system i would have to re-orient my camera to look at the system in the easiest way to get a sense of where things are located. Recall that Gal Civ is a game that keeps the map simple at its core. The move to 3D will just unnecessarily complicate matters, especially since solar systems live on planes anyway.
All Gal Civ 3 is doing is not showing the 3d variation or orientation to make things easier to read and see. Without this, I would always spend my time looking at a horizontal plane of the solar system no matter the orientation. I look at the exercise of benefits of 3d map vs. difficulty of use on the 3d maps. If our computers were designed to handle a 3d map, then movement and such would be soo much easier. But I suspect that technology is a long way off.